3-Substituted pyrazole analogs of the cannabinoid type 1 (CB1) receptor antagonist rimonabant: cannabinoid agonist-like effects in mice via non-CB1, non-CB2 mechanism.

The prototypic cannabinoid type 1 (CB1) receptor antagonist/inverse agonist, rimonabant, is comprised of a pyrazole core surrounded by a carboxyamide with terminal piperidine group (3-substituent), a 2,4-dichlorophenyl group (1-substituent), a 4-chlorophenyl group (5-substituent), and a methyl group (4-substituent). Previous structure-activity relationship (SAR) analysis has suggested that the 3-position may be involved in receptor recognition and agonist activity. The goal of the present study was to develop CB1-selective compounds and explore further the SAR of 3-substitution on the rimonabant template. 3-Substituted analogs with benzyl and alkyl amino, dihydrooxazole, and oxazole moieties were synthesized and evaluated in vitro and in vivo. Several notable patterns emerged. First, most of the analogs exhibited CB1 selectivity, with many lacking affinity for the CB2 receptor. Affinity tended to be better when [³H]5-(4-chlorophenyl)-1-(2,4-dichloro-phenyl)-4-methyl-N-(piperidin-1-yl)-1H-pyrazole-3-carboxamide (SR141716), rather than [³H](-)-cis-3-[2-hydroxy-4(1,1-dimethyl-heptyl)phenyl]-trans-4-(3-hydroxy-propyl)cyclohexanol (CP55,940), was used as the binding radioligand. Second, many of the analogs produced an agonist-like profile of effects in mice (i.e., suppression of activity, antinociception, hypothermia, and immobility); however, their potencies were not well correlated with their CB1 binding affinities. Further assessment of selected analogs showed that none were effective antagonists of the effects of Δ9-tetrahydrocannabinol in mice, their agonist-like effects were not blocked by rimonabant, they were active in vivo in CB1⁻/⁻ mice, and they failed to stimulate guanosine-5'-O-(3-[³5S]thio)-triphosphate binding. Several analogs were inverse agonists in the latter assay. Together, these results suggest that this series of 3-substituted pyrazole analogs represent a novel class of CB1-selective cannabinoids that produce agonist-like effects in mice through a non-CB1, non-CB2 mechanism.

Medline search engine for finding genetic markers with biological significance.

MOTIVATION: Genome-wide high density SNP association studies are expected to identify various SNP alleles associated with different complex disorders. Understanding the biological significance of these SNP alleles in the context of existing literature is a major challenge since existing search engines are not designed to search literature for SNPs or other genetic markers. The literature mining of gene and protein functions has received significant attention and effort while similar work on genetic markers and their related diseases is still in its infancy. Our goal is to develop a web-based tool that facilitates the mining of Medline literature related to genetic studies and gene/protein function studies. Our solution consists of four main function modules for (1) identification of different types of genetic markers or genetic variations in Medline records (2) distinguishing positive versus negative linkage or association between genetic markers and diseases (3) integrating marker genomic location data from different databases to enable the retrieval of Medline records related to markers in the same linkage disequilibrium region (4) and a web interface called MarkerInfoFinder to search, display, sort and download Medline citation results. Tests using published data suggest MarkerInfoFinder can significantly increase the efficiency of finding genetic disorders and their underlying molecular mechanisms. The functions we developed will also be used to build a knowledge base for genetic markers and diseases. AVAILABILITY: The MarkerInfoFinder is publicly available at: http://brainarray.mbni.med.umich.edu/brainarray/datamining/MarkerInfoFinder.

Web-based GeneChip analysis system for large-scale collaborative projects.

UNLABELLED: The Web-Based GeneChip Analysis System (WGAS) is developed to overcome limitations in analysis setup efficiency, data and procedure sharing, as well as security issues in existing commercial and public domain solutions. It also incorporates unique functions and resources for more accurate and flexible GeneChip analysis. AVAILABILITY: WGAS is freely available at: http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html.

SNP Function Portal: a web database for exploring the function implication of SNP alleles.

MOTIVATION: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as the related functional data are distributed across many different databases. The SNP Function Portal is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, the SNP Function Portal includes a powerful search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, our system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments. AVAILABILITY: http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx.

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals approximately 30-50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions.

Synthesis and evaluation of dopamine and serotonin transporter inhibition by oxacyclic and carbacyclic analogues of methylphenidate.

Methylphenidate (Ritalin) binds stereoselectively and enantioselectively to the dopamine transporter (DAT) and inhibits dopamine reuptake with in vitro and in vivo potency similar to that of cocaine. Unlike cocaine, it manifests little, if any, tolerance or addiction liability. Since this compound has a substantial clinical history, it provides an excellent template from which to design potential medications for cocaine abuse. It has long been assumed that a nitrogen, such as exists in cocaine and methylphenidate, is essential for interaction with monoamine transporters. We previously demonstrated that an amine nitrogen in phenyltropane analogues of cocaine is not necessary for conferring high DAT binding affinity. We now report the synthesis of oxacyclic and carbacyclic analogues of methylphenidate, including the four enantiomerically pure isomers of 2-(3,4-dichlorophenyl)-2-(tetrahydropyran-2-yl)acetic acid methyl ester. The threo isomers are potent and selective inhibitors of the DAT. This is the first generalization of the principle that the presence of nitrogen is not a necessity for DAT inhibition.

ProbeMatchDB--a web database for finding equivalent probes across microarray platforms and species.

SUMMARY: ProbeMatchDB is a web-based database designed to facilitate the search of EST/cDNA sequences or STS markers that can be used to represent the same gene across different microarray platforms and species. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. AVAILABILITY: The database is accessible at http://brainarray.mhri.med.umich.edu/MARRAY/BC_ASP/brainarray.htm by clicking the 'Query ProbeMatchDB' link.